Wrapper Functions for 'FreeSurfer'

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Documentation for package ‘freesurfer’ version 1.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A C E F G H M N R S T

-- A --

aparcstats2table	Generalized Stats to Table
aparcstats2table.help	Generalized Stats to Table
aparcs_to_bg	Convert Freesurfer aparcs Table to brainGraph
asegstats2table	Generalized Stats to Table
asegstats2table.help	Generalized Stats to Table
autorecon1	Manual Freesurfer Reconstruction Workflow
autorecon2	Manual Freesurfer Reconstruction Workflow
autorecon3	Manual Freesurfer Reconstruction Workflow

-- C --

checkmnc	Force object to filename with .mnc extension
checkmnc-method	Force object to filename with .mnc extension
checkmnc-methods	Force object to filename with .mnc extension
construct_subj_dir	Construct Subject Directory
convert_surface	Convert Freesurfer Surface

-- E --

ensure_mnc

Force object to filename with .mnc extension

-- F --

freesurferdir	Get FreeSurfer Directory Paths
freesurfer_dir	Get FreeSurfer Directory Paths
freesurfer_read_curv	Read Freesufer Curv file
freesurfer_read_surf	Read Freesurfer Surface file
fs_cmd	Execute FreeSurfer Commands from R
fs_dir	Get FreeSurfer Directory Paths
fs_flag_cmd	Run a Flag-Based FreeSurfer Command
fs_help	Wrapper for getting FreeSurfer help
fs_imgext	Determine extension of image based on Freesurfer output type
fs_lut	Freesurfer look up table (LUT)
fs_sitrep	FreeSurfer Situation Report
fs_subj_dir	Get FreeSurfer Directory Paths
fs_version	Find Freesurfer Version

-- G --

get_fs	Generate FreeSurfer Command Line Environment Setup
get_fs_home	Retrieve FreeSurfer Configuration Settings
get_fs_license	Retrieve FreeSurfer Configuration Settings
get_fs_output	Retrieve FreeSurfer Configuration Settings
get_fs_setting	Retrieve FreeSurfer Configuration Settings
get_fs_source	Retrieve FreeSurfer Configuration Settings
get_fs_subdir	Retrieve FreeSurfer Configuration Settings
get_fs_verbosity	Retrieve FreeSurfer Configuration Settings
get_mni_bin	Retrieve FreeSurfer Configuration Settings

-- H --

have_fs

Logical check if Freesurfer is accessible

-- M --

mnc2nii	Convert MNC to NIfTI
mnc2nii.help	Convert MNC to NIfTI
mris_convert	Convert Cortical Surface File Formats with FreeSurfer
mris_convert.help	Convert Cortical Surface File Formats with FreeSurfer
mris_convert_annot	Convert Cortical Surface File Formats with FreeSurfer
mris_convert_curv	Convert Cortical Surface File Formats with FreeSurfer
mris_convert_normals	Convert Cortical Surface File Formats with FreeSurfer
mris_convert_vertex	Convert Cortical Surface File Formats with FreeSurfer
mris_euler_number	MRIs Euler Number
mris_euler_number.help	MRI Euler Number Help
mri_convert	Convert Medical Image Formats with FreeSurfer
mri_convert.help	Convert Medical Image Formats with FreeSurfer
mri_deface	MRI Deface
mri_info	MRI information
mri_info.help	MRI information Help
mri_mask	Use Freesurfers MRI Mask
mri_mask.help	MRI Normalize Help
mri_normalize	Use Freesurfers MRI Normalize Algorithm
mri_normalize.help	MRI Normalize Help
mri_segment	Use Freesurfers MRI Segmentation Algorithm
mri_segment.help	Use Freesurfers MRI Segmentation Algorithm
mri_surf2surf	Resample Cortical Surface Data with FreeSurfer
mri_surf2surf.help	Resample Cortical Surface Data with FreeSurfer
mri_synthstrip	Use Freesurfers MRI SynthStrip
mri_synthstrip.help	MRI Normalize Help
mri_vol2vol	Resample a Volume into Another Volume's Space with FreeSurfer
mri_vol2vol.help	Resample a Volume into Another Volume's Space with FreeSurfer
mri_watershed	Use Freesurfers MRI Watershed Algorithm
mri_watershed.help	Use Freesurfers MRI Watershed Algorithm

-- N --

nii2mnc	Convert NIfTI to MNC
nii2mnc.help	Convert NIfTI to MNC
nu_correct	Use FreeSurfer's Non-Uniformity Correction
nu_correct.help	Use FreeSurfer's Non-Uniformity Correction

-- R --

readmgh	Read MGH or MGZ File
readmgz	Read MGH or MGZ File
read_annotation	Read Freesurfer annotation file
read_aseg_stats	Read FreeSurfer Anatomical Segmentation Statistics
read_fs_label	Read Label File
read_fs_table	Read FreeSurfer Table Output
read_mgh	Read MGH or MGZ File
read_mgz	Read MGH or MGZ File
read_mnc	Read MNC File
read_stats_table	Read FreeSurfer Table Output
recon	FreeSurfer Reconstruction Pipeline Functions
reconner	Reconstruction Helper for FreeSurfer's recon-all
recon_all	FreeSurfer Reconstruction Pipeline Functions
recon_con1	Manual Freesurfer Reconstruction Workflow
recon_con2	Manual Freesurfer Reconstruction Workflow
recon_con3	Manual Freesurfer Reconstruction Workflow
recon_manual	Manual Freesurfer Reconstruction Workflow
recon_steps	FreeSurfer Reconstruction Pipeline Functions

-- S --

stats2table	Generalized Stats to Table
surface_to_obj	Convert Freesurfer Surface to Wavefront OBJ
surface_to_triangles	Convert Freesurfer Surface to Triangles
surf_convert	Convert Surface Data to ASCII
synthstrip	Use Freesurfers MRI SynthStrip

-- T --

temp_file	Create a Temporary File with a Newly Created Directory
trac	FreeSurfer Diffusion Tractography Pipeline
tracker	FreeSurfer Diffusion Tractography Pipeline
tracker.help	FreeSurfer Diffusion Tractography Pipeline
trac_all	FreeSurfer Diffusion Tractography Pipeline
trac_bedpost	FreeSurfer Diffusion Tractography Pipeline
trac_path	FreeSurfer Diffusion Tractography Pipeline
trac_prep	FreeSurfer Diffusion Tractography Pipeline